Mitochondrial dysfunction is the major mechanism precipitating ischemia/reperfusion (I/R) injury which commonly occurs during liver surgery, trauma, hemorrhagic shock and liver transplantation. Mitochondrial autophagy (mitophagy) is the only cellular process that selectively removes abnormal mitochondria. The contribution of mitophagy to liver injury after warm ischemia is unknown. The goal of this study is to elucidate the mechanisms underlying lethal I/R injury to liver and to develop therapeutic strategies to improve liver function after I/R. In preliminary studies, we observed the loss of Atg7 and Beclin-1, key mitophagy proteins, after I/R. We have shown that Ca2+ overloading after I/R stimulates calpain isoform-2 and that activated calpain-2 degrades Atg7 and Beclin-1. Suppression of mitophagy protein depletion prevents onset of the mitochondrial permeability transition (MPT), hepatocellular necrosis and apoptosis, and protects mitochondrial function after I/R. Furthermore, we noted that loss of mitophagy proteins occurs in an in vivo model of hepatic I/R in mice, concomitant with mitochondrial depolarization and cell death. We propose that I/R impairs mitophagy, which in turn leads to accumulation of dysfunctional mitochondria and ultimately hepatic failure. Therefore, restoration or enhancement of mitophagy in ischemic liver will promote the clearance of dysfunctional mitochondria and consequently ameliorate liver dysfunction after reperfusion. Our principle hypothesis is that Ca2+ overloading causes increased calpain-2 activity that subsequently results in hydrolyzation of key mitophagy proteins leading to impaired mitophagy and MPT-dependent hepatocyte death after I/R. These studies provide critical mechanistic insights into lethal I/R injury to liver, and will establish novel therapeutic approaches for improving I/R-mediated liver failure.